ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2014
Identification of TNF-α-responsive promoters and enhancers in the intestinal epithelial cell model Caco-2.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed, 11 citations in OpenAlex.
- The RNA exosome shapes the expression of key protein-coding genes.Nucleic acids research · 2020Article
- Comprehensive profiling of the fission yeast transcription start site activity during stress and media response.Nucleic acids research · 2019Article
- The RNA exosome contributes to gene expression regulation during stem cell differentiation.Nucleic acids research · 2018Article
- Intestinal regulation of suppression of tumorigenicity 14 (ST14) and serine peptidase inhibitor, Kunitz type -1 (SPINT1) by transcription factor CDX2.Scientific reports · 2018Article
- Characterization of the enhancer and promoter landscape of inflammatory bowel disease from human colon biopsies.Nature communications · 2018Article
- Transcriptional Regulation of the Ambient Temperature Response by H2A.Z Nucleosomes and HSF1 Transcription Factors in Arabidopsis.Molecular plant · 2017Article
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Authors and funding
14 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The Caco-2 cell line is one of the most important in vitro models for enterocytes, and is used to study drug absorption and disease, including inflammatory bowel disease and cancer. In order to use the model optimally, it is necessary to map its functional entities. In this study, we have generated genome-wide maps of active transcription start sites (TSSs), and active enhancers in Caco-2 cells with or without tumour necrosis factor (TNF)-α stimulation to mimic an inflammatory state. We found 520 promoters that significantly changed their usage level upon TNF-α stimulation; of these, 52% are not annotated. A subset of these has the potential to confer change in protein function due to protein domain exclusion. Moreover, we locate 890 transcribed enhancer candidates, where ∼50% are changing in usage after TNF-α stimulation. These enhancers share motif enrichments with similarly responding gene promoters. As a case example, we characterize an enhancer regulating the laminin-5 γ2-chain (LAMC2) gene by nuclear factor (NF)-κB binding. This report is the first to present comprehensive TSS and enhancer maps over Caco-2 cells, and highlights many novel inflammation-specific promoters and enhancers.
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